RE: Failure to execute NONMEM from R

-----Original Message----- From: Tarj Sahota [mailto:[email protected]] Sent: Thursday, December 21, 2017 10:18 PM To: Devin Pastoor <[email protected]> Cc: HUI, Ka Ho <[email protected]>; Bill Denney <[email protected]>; [email protected] Subject: Re: [NMusers] Failure to execute NONMEM from R I get the same errors as Matthew (with NM 7.4.1+gfortran on windows) - I forgot to mention that in order to get it working on my machine I also need to use shell() rather than system()/system2()/... along with Sys.unsetenv("GFORTRAN_STDOUT_UNIT"). Not sure if that helps you, but it fixes the issue with my windows machine. Tarj. On Thu, Dec 21, 2017 at 11:49 AM, Devin Pastoor <[email protected]> wrote: > I believe the problem is actually that is cross referenced > http://discuss.go-isop.org/t/psn-execute-failed-to-start-when-called-f > rom-rstudio/1119 > It is not a path issue > > Mike and I have had a small amount of offline exploration and can > confirm it a pervasive issue with NM74 being called from Rstudio. This > is not just PsN, I also use a separate language (go) to manage the > nmfe commands and invoking that from Rstudio via system2/processx/sys > all fails in the same fashion. At this point, I believe it is likely a > permissions issue, but I am unsure of if the (primary) culprit is nonmem or > Rstudio. > > We will need to get Bob's input whether there was a change in the > mechanics of how nonmem is invoked from 73 --> 74 to hopefully narrow > the surface area of what could be causing the problem. > > On Wed, Dec 20, 2017 at 10:47 PM HUI, Ka Ho > <[email protected]> > wrote: >> >> Thanks for attending the problem, Bill. >> >> >> >> Exactly which path should I be looking for? Am I to check if the >> desired path exists in the list or not? >> >> I tried adding the paths for NONMEM, PsN, R and Rstudio into the list >> and executed commands in R again – nothing has changed so far. Any idea? >> >> >> >> Thanks, >> >> Matthew >> >> >> >> From: Bill Denney [mailto:[email protected]] >> Sent: Thursday, December 21, 2017 11:11 AM >> To: HUI, Ka Ho <[email protected]> >> Cc: [email protected] >> Subject: Re: [NMusers] Failure to execute NONMEM from R >> >> >> >> Hi Matthew, >> >> >> >> Since everything is working when run directly from the command line >> (cmd), I would guess that it's something like a path issue. >> >> >> >> Check your path at the command prompt (type "path") and in RStudio >> ("Sys.getenv("PATH")"). >> >> >> >> Thanks, >> >> >> >> Bill >> >> >> On Dec 20, 2017, at 21:54, HUI, Ka Ho <[email protected]> >> wrote: >> >> Dear NMusers, >> >> >> >> Recently I need to execute NONMEM 7.4 from Rstudio terminal. I have >> tried the following scripts: >> >> `system2(“execute FIT_01.mod”)` #Through PsN, >> using `system2` >> `shell(“execute FIT_01.mod”)` #Through >> PsN, using `shell` >> `write(“execute FIT_01.mod”, “FIT_01.bat”)` `shell(“FIT_01.bat”)` >> #Through PsN, using `shell` to call a batch file `write(“execute >> FIT_01.mod”, “FIT_01.bat”)` `shell.exec(“FIT_01.bat”)` #Through PsN, >> using `shell.exec` to call a batch file The above commands, but call >> through C:/nm74g64/run/nmfe74.bat directly >> >> >> >> The above were also tested using the test dataset `CONTROL5` >> >> >> >> Results: >> >> gave me the `running command '"execute FIT_01.mod"' had status 127` >> warning without any execution >> >> >> >> (2)-(4) gave me the following messages: >> >> Starting 1 NONMEM executions. 1 in parallel. >> S:1 .. >> All executions started. >> Starting NMTRAN >> NMtran failed. There is no output for model 1. Contents of FMSG: >> >> Not restarting this model. >> F:1 .. >> execute done >> >> (5) similar to (1) but the status/error code became 107 >> >> >> >> None of the above has led to a successful NONMEM run. But the above >> command lines work when outside R (i.e. through `cmd` +/- PsN) >> >> Is there anyone experiencing the same issue? >> >> >> >> System/software info: >> >> OS: Windows 10 >> >> NONMEM v7.4 >> >> R3.4.2 >> >> Rstudio v1.1.383 >> >> >> >> Best regards, >> >> Matthew Hui >> >> PhD Student >> >> School of Pharmacy >> >> Faculty of Medicine >> >> The Chinese University of Hong Kong >> >>